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Detailed information for vg0518701430:

Variant ID: vg0518701430 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 18701430
Reference Allele: GAlternative Allele: A,T
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.75, A: 0.25, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


TGCCAACGACGGGATGAATCCACATACCAACAGCAATTTGAATTGTTGAACTTGATTTTAAAGTTAATTTTGAGATGTTTTTAACGTAATTTTTTTTAAT[G/A,T]
TTGACTTTTAAGTCATTACGAATAAATCTATAAAAGTTTTACTTATAAATTAATTTTTATTTTTTAATAAGGCAAAACTGACAACCGATGGAAGCCCAAG

Reverse complement sequence

CTTGGGCTTCCATCGGTTGTCAGTTTTGCCTTATTAAAAAATAAAAATTAATTTATAAGTAAAACTTTTATAGATTTATTCGTAATGACTTAAAAGTCAA[C/T,A]
ATTAAAAAAAATTACGTTAAAAACATCTCAAAATTAACTTTAAAATCAAGTTCAACAATTCAAATTGCTGTTGGTATGTGGATTCATCCCGTCGTTGGCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 49.90% 49.60% 0.51% 0.02% NA
All Indica  2759 26.80% 72.40% 0.80% 0.04% NA
All Japonica  1512 96.60% 3.30% 0.07% 0.00% NA
Aus  269 3.00% 97.00% 0.00% 0.00% NA
Indica I  595 11.80% 87.70% 0.50% 0.00% NA
Indica II  465 33.80% 65.40% 0.86% 0.00% NA
Indica III  913 34.80% 64.40% 0.77% 0.00% NA
Indica Intermediate  786 24.70% 74.20% 1.02% 0.13% NA
Temperate Japonica  767 96.50% 3.50% 0.00% 0.00% NA
Tropical Japonica  504 96.00% 3.80% 0.20% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 3.10% 1.04% 0.00% NA
Intermediate  90 62.20% 37.80% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0518701430 G -> T LOC_Os05g32080.1 upstream_gene_variant ; 1157.0bp to feature; MODIFIER N Average:94.997; most accessible tissue: Minghui63 panicle, score: 99.257 N N N N
vg0518701430 G -> T LOC_Os05g32080-LOC_Os05g32090 intergenic_region ; MODIFIER N Average:94.997; most accessible tissue: Minghui63 panicle, score: 99.257 N N N N
vg0518701430 G -> DEL N N silent_mutation Average:94.997; most accessible tissue: Minghui63 panicle, score: 99.257 N N N N
vg0518701430 G -> A LOC_Os05g32080.1 upstream_gene_variant ; 1157.0bp to feature; MODIFIER silent_mutation Average:94.997; most accessible tissue: Minghui63 panicle, score: 99.257 N N N N
vg0518701430 G -> A LOC_Os05g32080-LOC_Os05g32090 intergenic_region ; MODIFIER silent_mutation Average:94.997; most accessible tissue: Minghui63 panicle, score: 99.257 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg0518701430 G A -0.02 0.0 0.0 -0.03 -0.03 -0.02
vg0518701430 G T -0.03 0.0 0.0 -0.03 -0.04 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0518701430 NA 5.06E-06 mr1884 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0518701430 NA 4.74E-07 mr1979 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0518701430 NA 6.41E-12 mr1986 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0518701430 NA 3.52E-06 mr1986 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0518701430 NA 1.25E-08 mr1004_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251